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Genome-wide association study

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https://www.readbyqxmd.com/read/29029276/complement-c3-associates-with-incidence-of-diabetes-but-no-evidence-of-a-causal-relationship
#1
Yan Borné, Iram Faqir Muhammad, Laura Lorés-Motta, Bo Hedblad, Peter M Nilsson, Olle Melander, Eiko K de Jong, Anna M Blom, Anneke I den Hollander, Gunnar Engström
Purpose: This study explored whether complement factor 3 (C3) in plasma is associated with incidence of diabetes in a population-based cohort. We also identified genetic variants related to C3 and explored whether C3 and diabetes share common genetic determinants. Methods: C3 was analyzed in plasma from 4368 non-diabetic subjects, 46-68 years old, from the Malmö Diet and Cancer study (MDC). Incidence of diabetes was studied in relation to C3 levels during 17.7±4...
September 29, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29029143/genome-wide-analysis-of-genetic-risk-factors-for-rheumatic-heart-disease-in-aboriginal-australians-provides-support-for-pathogenic-molecular-mimicry
#2
Lesley-Ann Gray, Heather A D'Antoine, Steven Y C Tong, Melita McKinnon, Dawn Bessarab, Ngaire Brown, Bo Reményi, Andrew Steer, Genevieve Syn, Jenefer M Blackwell, Michael Inouye, Jonathan R Carapetis
Background: Rheumatic heart disease (RHD) following Group A Streptococcus (GAS) infections is heritable and prevalent in Indigenous populations. Molecular mimicry between human and GAS proteins triggers pro-inflammatory cardiac valve-reactive T-cells. Methods: Genome-wide genetic analysis was undertaken in 1263 Aboriginal Australians (398 RHD cases; 865 controls). Single nucleotide polymorphisms (SNPs) were genotyped using Illumina HumanCoreExome BeadChips. Direct typing and imputation was used to fine-map the human leukocyte antigen (HLA) region...
September 26, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29028944/identification-and-replication-of-the-interplay-of-four-genetic-high-risk-variants-for-urinary-bladder-cancer
#3
Silvia Selinski, Meinolf Blaszkewicz, Katja Ickstadt, Holger Gerullis, Thomas Otto, Emanuel Roth, Frank Volkert, Daniel Ovsiannikov, Oliver Moormann, Gergely Banfi, Peter Nyirady, Sita H Vermeulen, Montserrat Garcia-Closas, Jonine D Figueroa, Alison Johnson, Margaret R Karagas, Manolis Kogevinas, Nuria Malats, Molly Schwenn, Debra T Silverman, Stella Koutros, Nathaniel Rothman, Lambertus A Kiemeney, Jan G Hengstler, Klaus Golka
Little is known whether genetic variants identified in genome-wide association studies interact to increase bladder cancer risk. Recently, we identified two- and three-variant combinations associated with a particular increase of bladder cancer risk in a urinary bladder cancer case-control series (IfADo, 1501 cases, 1565 controls). In an independent case-control series (Nijmegen Bladder Cancer Study, NBCS, 1468 cases, 1720 controls) we confirmed these two- and three-variant combinations. Pooled analysis of the two studies as discovery group (IfADo-NBCS) resulted in sufficient statistical power to test up to four-variant combinations by a logistic regression approach...
September 27, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/29028941/dysregulation-of-cortical-neuron-dna-methylation-profile-in-autism-spectrum-disorder
#4
Stefano Nardone, Dev Sharan Sams, Antonino Zito, Eli Reuveni, Evan Elliott
Autism Spectrum Disorder (ASD) is a complex neuropsychiatric syndrome whose etiology includes genetic and environmental components. Since epigenetic marks are sensitive to environmental insult, they may be involved in the development of ASD. Initial brain studies have suggested a dysregulation of epigenetic marks in ASD. However, due to cellular heterogeneity in the brain, these studies have not determined if there is a true change in the neuronal epigenetic signature. Here, we report a genome-wide methylation study on fluorescence-activated cell sorting-sorted neuronal nuclei from the frontal cortex of 16 male ASD and 15 male control subjects...
September 28, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/29028809/nasal-dna-methylation-differentiates-corticosteroid-treatment-response-in-pediatric-asthma-a-pilot-study
#5
Xue Zhang, Jocelyn M Biagini Myers, Veda K Yadagiri, Ashley Ulm, Xiaoting Chen, Matthew T Weirauch, Gurjit K Khurana Hershey, Hong Ji
BACKGROUND: Treatment response to systemic corticosteroid in asthmatic children is heterogeneous and may be mediated by epigenetic mechanism(s). We aim to identify DNA methylation (DNAm) changes responsive to steroid, and DNAm biomarkers that distinguish treatment response. MATERIALS AND METHODS: We followed 33 children (ages 5-18) presenting to the Emergency Department (ED) for asthma exacerbation. Based on whether they met discharge criteria in ≤24 hours, participants were grouped into good and poor responders to steroid treatment...
2017: PloS One
https://www.readbyqxmd.com/read/29027999/a-population-genomics-approach-shows-widespread-geographical-distribution-of-cryptic-genomic-forms-of-the-symbiotic-fungus-rhizophagus-irregularis
#6
Romain Savary, Frédéric G Masclaux, Tania Wyss, Germain Droh, Joaquim Cruz Corella, Ana Paula Machado, Joseph B Morton, Ian R Sanders
Arbuscular mycorrhizal fungi (AMF; phylum Gomeromycota) associate with plants forming one of the most successful microbe-plant associations. The fungi promote plant diversity and have a potentially important role in global agriculture. Plant growth depends on both inter- and intra-specific variation in AMF. It was recently reported that an unusually large number of AMF taxa have an intercontinental distribution, suggesting long-distance gene flow for many AMF species, facilitated by either long-distance natural dispersal mechanisms or human-assisted dispersal...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29027642/familial-mpn-predisposition
#7
REVIEW
Tsewang Tashi, Sabina Swierczek, Josef T Prchal
Chronic myeloproliferative neoplasms (MPN) characteristically arise from a somatic mutation in the pluripotent hematopoietic stem cell, and most common recurring mutations are in the JAK2, CALR, and cMPL genes. However, these mutations are not founder mutations, but mainly drive the disease phenotype and a pre-existing germline predisposition has been long speculated, but has not been clearly defined to date. Genome-wide association studies in family clusters of MPN have identified a number of genetic variants that are associated with increased germline risk for developing clonal MPN...
October 13, 2017: Current Hematologic Malignancy Reports
https://www.readbyqxmd.com/read/29027019/explorative-results-from-multistep-screening-for-potential-genetic-risk-loci-of-alzheimer-s-disease-in-the-longitudinal-vita-study-cohort
#8
Claus-Jürgen Scholz, Heike Weber, Susanne Jungwirth, Walter Danielczyk, Andreas Reif, Karl-Heinz Tragl, Peter Fischer, Peter Riederer, Jürgen Deckert, Edna Grünblatt
Alzheimer's disease (AD) is a neurodegenerative disorder that preferentially affects individuals of advanced age. Heritability estimates for AD range between 60 and 80%, but only few genetic risk factors have been identified so far. In the present explorative study, we aimed at characterizing the genetic contribution to late-onset AD in participants of the Vienna Transdanube Aging (VITA) longitudinal birth cohort study in a two-step approach. First, we performed a genome-wide screen of pooled DNA samples (n = 588) to identify allele frequency differences between AD patients and non-AD individuals using life-time diagnoses made at the age of 80 (t = 60 months)...
October 12, 2017: Journal of Neural Transmission
https://www.readbyqxmd.com/read/29026649/unique-genome-organization-of-non-mammalian-papillomaviruses-provides-insights-into-the-evolution-of-viral-early-proteins
#9
Koenraad Van Doorslaer, Valeria Ruoppolo, Annie Schmidt, Amelie Lescroël, Dennis Jongsomjit, Megan Elrod, Simona Kraberger, Daisy Stainton, Katie M Dugger, Grant Ballard, David G Ainley, Arvind Varsani
The family Papillomaviridae contains more than 320 papillomavirus types, with most having been identified as infecting skin and mucosal epithelium in mammalian hosts. To date, only nine non-mammalian papillomaviruses have been described from birds (n = 5), a fish (n = 1), a snake (n = 1), and turtles (n = 2). The identification of papillomaviruses in sauropsids and a sparid fish suggests that early ancestors of papillomaviruses were already infecting the earliest Euteleostomi. The Euteleostomi clade includes more than 90 per cent of the living vertebrate species, and progeny virus could have been passed on to all members of this clade, inhabiting virtually every habitat on the planet...
July 2017: Virus Evolution
https://www.readbyqxmd.com/read/29026448/newborn-genome-wide-dna-methylation-in-association-with-pregnancy-anxiety-reveals-a-potential-role-for-gabbr1
#10
Elise Beau Vangeel, Ehsan Pishva, Titia Hompes, Daniel van den Hove, Diether Lambrechts, Karel Allegaert, Kathleen Freson, Benedetta Izzi, Stephan Claes
BACKGROUND: There is increasing evidence for the role of prenatal stress in shaping offspring DNA methylation and disease susceptibility. In the current study, we aimed to identify genes and pathways associated with pregnancy anxiety using a genome-wide DNA methylation approach. METHODS: We selected 22 versus 23 newborns from our Prenatal Early Life Stress (PELS) cohort, exposed to the lowest or highest degree of maternal pregnancy anxiety, respectively. Cord blood genome-wide DNA methylation was assayed using the HumanMethylation450 BeadChip (HM450, n = 45) and candidate gene methylation using EpiTYPER (n = 80)...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/29026206/genome-wide-association-studies-of-cancer-current-insights-and-future-perspectives
#11
REVIEW
Amit Sud, Ben Kinnersley, Richard S Houlston
Genome-wide association studies (GWAS) provide an agnostic approach for investigating the genetic basis of complex diseases. In oncology, GWAS of nearly all common malignancies have been performed, and over 450 genetic variants associated with increased risks have been identified. As well as revealing novel pathways important in carcinogenesis, these studies have shown that common genetic variation contributes substantially to the heritable risk of many common cancers. The clinical application of GWAS is starting to provide opportunities for drug discovery and repositioning as well as for cancer prevention...
October 13, 2017: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/29026147/vascular-endothelial-growth-factor-in-cartilage-development-and-osteoarthritis
#12
Masashi Nagao, John L Hamilton, Ranjan Kc, Agnes D Berendsen, Xuchen Duan, Chan Wook Cheong, Xin Li, Hee-Jeong Im, Bjorn R Olsen
Genome wide studies indicate that vascular endothelial growth factor A (VEGF) is associated with osteoarthritis (OA), and increased VEGF expression correlates with increased disease severity. VEGF is also a chondrocyte survival factor during development and essential for bone formation, skeletal growth and postnatal homeostasis. This raises questions of how the important embryonic and postnatal functions of VEGF can be reconciled with an apparently destructive role in OA. Addressing these questions, we find that VEGF acts as a survival factor in growth plate chondrocytes during development but only up until a few weeks after birth in mice...
October 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29025893/disease-specific-biases-in-alternative-splicing-and-tissue-specific-dysregulation-revealed-by-multitissue-profiling-of-lymphocyte-gene-expression-in-type-1-diabetes
#13
Jeremy R B Newman, Ana Conesa, Matthew Mika, Felicia N New, Suna Onengut-Gumuscu, Mark A Atkinson, Stephen S Rich, Lauren M McIntyre, Patrick Concannon
Genome-wide association studies (GWAS) have identified multiple, shared allelic associations with many autoimmune diseases. However, the pathogenic contributions of variants residing in risk loci remain unresolved. The location of the majority of shared disease-associated variants in noncoding regions suggests they contribute to risk of autoimmunity through effects on gene expression in the immune system. In the current study, we test this hypothesis by applying RNA sequencing to CD4(+), CD8(+), and CD19(+) lymphocyte populations isolated from 81 subjects with type 1 diabetes (T1D)...
October 12, 2017: Genome Research
https://www.readbyqxmd.com/read/29025761/genome-wide-association-study-to-find-modifiers-for-tetralogy-of-fallot-in-the-22q11-2-deletion-syndrome-identifies-variants-in-the-gpr98-locus-on-5q14-3
#14
Tingwei Guo, Gabriela M Repetto, Donna M McDonald McGinn, Jonathan H Chung, Hiroko Nomaru, Christopher L Campbell, Anna Blonska, Anne S Bassett, Eva W C Chow, Elisabeth E Mlynarski, Ann Swillen, Joris Vermeesch, Koen Devriendt, Doron Gothelf, Miri Carmel, Elena Michaelovsky, Maude Schneider, Stephan Eliez, Stylianos E Antonarakis, Karlene Coleman, Aoy Tomita-Mitchell, Michael E Mitchell, M Cristina Digilio, Bruno Dallapiccola, Bruno Marino, Nicole Philip, Tiffany Busa, Leila Kushan-Wells, Carrie E Bearden, Małgorzata Piotrowicz, Wanda Hawuła, Amy E Roberts, Flora Tassone, Tony J Simon, Esther D A van Duin, Thérèse A van Amelsvoort, Wendy R Kates, Elaine Zackai, H Richard Johnston, David J Cutler, A J Agopian, Elizabeth Goldmuntz, Laura E Mitchell, Tao Wang, Beverly S Emanuel, Bernice E Morrow
BACKGROUND: The 22q11.2 deletion syndrome (22q11.2DS; DiGeorge syndrome/velocardiofacial syndrome) occurs in 1 of 4000 live births, and 60% to 70% of affected individuals have congenital heart disease, ranging from mild to severe. In our cohort of 1472 subjects with 22q11.2DS, a total of 62% (n=906) have congenital heart disease and 36% (n=326) of these have tetralogy of Fallot (TOF), comprising the largest subset of severe congenital heart disease in the cohort. METHODS AND RESULTS: To identify common genetic variants associated with TOF in individuals with 22q11...
October 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/29025760/prediction-for-intravenous-immunoglobulin-resistance-by-using-weighted-genetic-risk-score-identified-from-genome-wide-association-study-in-kawasaki-disease
#15
Ho-Chang Kuo, Henry Sung-Ching Wong, Wei-Pin Chang, Ben-Kuen Chen, Mei-Shin Wu, Kuender D Yang, Kai-Sheng Hsieh, Yu-Wen Hsu, Shih-Feng Liu, Xiao Liu, Wei-Chiao Chang
BACKGROUND: Intravenous immunoglobulin (IVIG) is the treatment of choice in Kawasaki disease (KD). IVIG is used to prevent cardiovascular complications related to KD. However, a proportion of KD patients have persistent fever after IVIG treatment and are defined as IVIG resistant. METHODS AND RESULTS: To develop a risk scoring system based on genetic markers to predict IVIG responsiveness in KD patients, a total of 150 KD patients (126 IVIG responders and 24 IVIG nonresponders) were recruited for this study...
October 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/29025430/genetic-architecture-of-lipid-traits-in-the-hispanic-community-health-study-study-of-latinos
#16
Mariaelisa Graff, Leslie S Emery, Anne E Justice, Esteban Parra, Jennifer E Below, Nicholette D Palmer, Chuan Gao, Qing Duan, Adan Valladares-Salgado, Miguel Cruz, Alanna C Morrison, Eric Boerwinkle, Eric A Whitsel, Charles Kooperberg, Alex Reiner, Yun Li, Carlos Jose Rodriguez, Gregory A Talavera, Carl D Langefeld, Lynne E Wagenknecht, Jill M Norris, Kent D Taylor, George Papanicolaou, Eimear Kenny, Ruth J F Loos, Yii-Der Ida Chen, Cathy Laurie, Tamar Sofer, Kari E North
BACKGROUND: Despite ethnic disparities in lipid profiles, there are few genome-wide association studies investigating genetic variation of lipids in non-European ancestry populations. In this study, we present findings from genetic association analyses for total cholesterol, low density lipoprotein cholesterol (LDL), high density lipoprotein cholesterol (HDL), and triglycerides in a large Hispanic/Latino cohort in the U.S., the Hispanic Community Health Study / Study of Latinos (HCHS/SOL)...
October 12, 2017: Lipids in Health and Disease
https://www.readbyqxmd.com/read/29025411/maize-rna-poliv-affects-the-expression-of-genes-with-nearby-te-insertions-and-has-a-genome-wide-repressive-impact-on-transcription
#17
Cristian Forestan, Silvia Farinati, Riccardo Aiese Cigliano, Alice Lunardon, Walter Sanseverino, Serena Varotto
BACKGROUND: RNA-directed DNA methylation (RdDM) is a plant-specific epigenetic process that relies on the RNA polymerase IV (Pol IV) for the production of 24 nucleotide small interfering RNAs (siRNA) that guide the cytosine methylation and silencing of genes and transposons. Zea mays RPD1/RMR6 gene encodes the largest subunit of Pol IV and is required for normal plant development, paramutation, transcriptional repression of certain transposable elements (TEs) and transcriptional regulation of specific alleles...
October 12, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29024823/genetic-variations-of-gwas-identified-genes-and-neuroblastoma-susceptibility-a-replication-study-in-southern-chinese-children
#18
Jing He, Yan Zou, Tongmin Wang, Ruizhong Zhang, Tianyou Yang, Jinhong Zhu, Fenghua Wang, Huimin Xia
Neuroblastoma is one of the most commonly diagnosed solid cancers for children, and genetic factors may play a critical role in neuroblastoma development. Previous genome-wide association studies (GWASs) have identified nine genes associated with neuroblastoma susceptibility in Caucasians. To determine whether genetic variations in these genes are also associated with neuroblastoma susceptibility in Southern Chinese children, we genotyped 25 polymorphisms within these genes by the TaqMan method in 256 cases and 531 controls...
October 9, 2017: Translational Oncology
https://www.readbyqxmd.com/read/29024729/integrating-genome-wide-association-study-and-expression-quantitative-trait-locus-study-identifies-multiple-genes-and-gene-sets-associated-with-schizophrenia
#19
Yan Zhao, Awen He, Feng Zhu, Miao Ding, Jingcan Hao, Qianrui Fan, Ping Li, Li Liu, Yanan Du, Xiao Liang, Xiong Guo, Feng Zhang, Xiancang Ma
Schizophrenia is a serious mental disease with high heritability. To better understand the genetic basis of schizophrenia, we conducted a large scale integrative analysis of genome-wide association study (GWAS) and expression quantitative trait loci (eQTLs) data. GWAS summary data was derived from a published GWAS of schizophrenia, containing 9394 schizophrenia patients and 12,462 healthy controls. The eQTLs dataset was obtained from an eQTLs meta-analysis of 5311 subjects, containing 923,021 cis-eQTLs for 14,329 genes and 4732 trans-eQTLs for 2612 genes...
October 9, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/29024632/quantitative-proteome-analysis-of-bovine-mammary-gland-reveals-protein-dynamic-changes-involved-in-peak-and-late-lactation-stages
#20
Xianrui Zheng, Chao Ning, Yichun Dong, Pengju Zhao, Junhui Li, Ziyao Fan, Jiang Li, Ying Yu, Raphael Mrode, Jian-Feng Liu
Mammary gland is an important organ for milk synthesis and secretion. It undergoes dramatic physiological changes to adapt the shift from peak to late lactation stage. Protein plays a final very vital role in many life functions, and the protein changes during different lactation stages potentially reflect the biology of lactation and the functions of mammary gland in cows. In current study, we adopted tandem mass tags label-based quantitative analysis technique and to investigate proteome changes occurring in bovine mammary gland from peak to late lactation stages...
October 9, 2017: Biochemical and Biophysical Research Communications
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